The quantitative evaluation of the heavy metal waste output from marine fish farming can provide scientific data for improving industrial planning and farming management of aquaculture. In this study, we analyzed contents of iron (Fe), copper (Cu), manganese (Mn), chromium (Cr), cadmium (Cd), and lead (Pb) in 48 samples of formulated feed and 144 samples large yellow croaker (Larimichthys crocea) whole-fish collected from six net-pen feeding trials, and determined the retention efficiency and waste outputs of the heavy-metals for the first time using a modified nutritional model that has been widely used for assessing nitrogen (N) and phosphorus (P) waste outputs of fish farming. The results showed that, the sequences were Mn (709.284 mg/kg)＞Fe (175.154 mg/kg)＞ Cu (34.215 mg/kg)＞Pb (7.339 mg/kg)＞Cr (0.688 mg/kg)＞Cd (0.413 mg/kg) for the content of the heavy-metals in the feed, Fe (10.187 mg/kg)＞Mn (2.392 mg/kg)＞Cu (0.581 mg/kg)＞Cr (0.464 mg/kg)＞Cd (0.014 mg/kg)＞Pb (0.013 mg/kg) for the content of the heavy-metals in the whole-fish body, Fe (6.36%)＞Cr (5.71%)＞Cd (4.58%)＞Pb (2.90%)＞Cu (1.75%)＞Mn (0.35%) for the retention efficiency of the heavy-metals, and Mn [0.9764 g/kg fish gain]＞Fe [0.1990 g/kg fish gain]＞Cu [0.0422 g/kg fish gain]＞Cr [0.0081 g/kg fish gain]＞Pb [0.0007 g/kg fish gain]＞Cd [0.0004 g/kg fish gain] for the waste outputs of fish farming. The heavy-metal contents depended on either the heavy-metal content in the feed or the retention efficiency of the heavy metals. Fe and Cr in whole-fish bodies were mainly affected by retention efficiency of these elements, while contents of Mn, Cu, Pb, and Cd in whole-fish were mainly affected by the feed content of these elements. The waste outputs of Fe, Cu, and Mn significantly positively correlated to wastes of N and P, respectively, suggesting that the wastes of Fe, Cu, and Mn increased with the increase of wastes of N and P. Considering the critical roles of N, P, and Fe as the nutrients limiting growth of phytoplankton and primary productivity in ocean, the results indicated that waste outputs of offshore aquaculture of large yellow croaker could remarkably elevate biomass of phytoplankton and primary productivity in ocean.